MolNFT v1 · #134823 · protein
Crystal structure of putative beta-lactamase from bacteroides dorei dsm 17855
5TGF · Uncharacterized protein: “Crystal structure of putative beta-lactamase from bacteroides dorei dsm 17855”. X-ray diffraction, 1 ligand (CA), 9 pockets (best druggability 0.69). MolNFT v1 #134823 on GenesisL1: 3D structure, binding…
- PDB
- 5TGF
- Type
- protein
- Length
- 1,331 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- B6VTD5
- Ligands
- CA
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Uncharacterized protein | protein | 333 | 36% helix, 16% strand | B6VTD5 |
| D | Uncharacterized protein | protein | 332 | 36% helix, 16% strand | B6VTD5 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains C, D
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.69 | 0.79 | 45 | empty |
| 2 | 558 | 0.66 | 0.76 | 77 | GOL |
| 3 | 401 | 0.65 | 0.79 | 70 | GOL |
| 4 | 513 | 0.63 | 0.76 | 55 | empty |
| 5 | 131 | 0.42 | 0.76 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–B · 561 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 546 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 244 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 242 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 5TGF · Crystal structure of putative beta-lactamase from Bacteroides dorei DSM 17855 · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt B6VTD5
- Elsewhere: RCSB PDB 5TGF · PDBe 5TGF · UniProt B6VTD5
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